ó
Ç™xTc           @   s:  d  d l  m Z d  d l Z d  d l m Z d  d l m Z d  d l m Z d  d l m	 Z	 d  d l
 m Z d  d l m Z d  d	 l m Z d  d
 l m Z d  d l m Z d  d l Z e j j d ƒ Z d  d l Td  d l Z e j j d ƒ Z d  d l Td e f d „  ƒ  YZ d „  Z d „  Z d „  Z d „  Z d S(   iÿÿÿÿ(   t   divisionN(   t   flex(   t   van_der_waals_radii(   t   maptbx(   t   crystal(   t   approx_equal(   t   miller(   t   fftpack(   t   matrix(   t   wk1995t   mmtbx_max_lik_ext(   t   *t   mmtbx_masks_extt   ordered_solvent_distributionc           B   s_   e  Z d d d d d d  d „ Z d „  Z d „  Z d „  Z d „  Z d d „ Z d d „ Z	 RS(	   iÿÿÿÿc         C   s¼   | | g j  d  ƒ d k s! t ‚ | d  k	 s3 t ‚ | d  k	 sE t ‚ | |  _ | |  _ | |  _ | |  _ | |  _ d  |  _ d  |  _	 d  |  _
 | d  k r¥ d |  _ n	 | |  _ |  j ƒ  d  S(   Ni   g      ð?(   t   countt   Nonet   AssertionErrort   n_realt   nshellst
   _structuret
   _grid_stept   _fot   _ft   _fct   _distributiont   radt   _f_ordered_solvent(   t   selft	   structuret   fot	   grid_stepR   R   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   __init__   s    !									c         C   sÿ  |  j  } | j d |  j ƒ j ƒ  } | |  _ |  j d  k ro t j d |  j j	 ƒ  d |  j
 ƒ } | j ƒ  } n	 |  j } t j ƒ  } t j ƒ  } g  } x] |  j j ƒ  D]L } | j t | j ƒ ƒ | j t j j | j ƒ  ƒ | j | j ƒ  ƒ q¦ W| j ƒ  | j ƒ  k st ‚ t j | j ƒ  d ƒ }	 |	 j ƒ  | j ƒ  k sJt ‚ t ƒ  |  _ |  j j d d d | d | d	 | d
 |  j j	 ƒ  d |  j j ƒ  d | d |	 d |  j d |  j ƒ 
|  j j ƒ  }
 t  |
 |  j | ƒ } t j! j" d |  j j# ƒ  j$ ƒ  d t% d | j& ƒ  d | d t' ƒ } t( j) d t( j* d t+ j, d |  j j	 ƒ  d |  j j# ƒ  ƒ d | j& ƒ  d t% ƒ d | j ƒ  ƒ |  _- | j& ƒ  j. |  j- j& ƒ  ƒ d k sªt ‚ | j& ƒ  j. | j& ƒ  ƒ d k sÑt ‚ t j/ t0 |  j- ƒ j ƒ  ƒ d k  sût ‚ |  S(   Nt   xray_structuret	   unit_cellt   stepi   t   shellg        t   xyzft   atmradt   element_symbolt   uct   sgt   nxnynzt   sel_flagR   R   t   space_groupt   anomalous_flagt   miller_indicest   complex_mapt   conjugate_flagt
   miller_sett   crystal_symmetryt   space_group_infot   indicest   datag      ð?(1   R   t!   structure_factors_from_scatterersR   t   f_calcR   R   R   R   t   crystal_griddingR!   R   R   t   vec3_doublet   doublet
   scattererst   appendt   listt   siteR   t   vdwt   tableR&   t   sizeR   t   intt   wat_distR   t   do_wat_distR+   R   R   R4   t   map_of_coeff_scaledt   structure_factorst   from_mapR2   t   groupt   FalseR3   t   TrueR   t   arrayt   setR   t   symmetryR   t   all_eqt   maxt   abs(   R   R   t   fcR7   R   R$   R%   t   elementst	   scattererR*   R4   t   map_of_coeffRF   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyR   2   sh    				
						*'*c         C   s   |  j  j ƒ  S(   N(   R   t   max_number_of_shells(   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyRT   ~   s    c         C   s   |  j  S(   N(   R   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   fcalc_from_distribution�   s    c         C   s   |  j  j ƒ  S(   N(   R   R4   (   R   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   distribution_as_array’   s    c         C   s/   | d  k	 r+ |  j j |  j j ƒ  | ƒ n  d  S(   N(   R   R   t   as_xplor_mapR   R!   (   R   t	   file_name(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   distribution_as_xplor_file•   s    c         C   sr  | d  k	 rnt | d ƒ } |  j j ƒ  } |  j j ƒ  } |  j j ƒ  } t |  j ƒ j ƒ  } |  j j ƒ  j ƒ  } t |  j ƒ j ƒ  } |  j j ƒ  j ƒ  }	 t |  j ƒ j ƒ  }
 d } x´ t	 | j
 ƒ  ƒ D]� } | j | | | d | | d | | d | | | | | | d | | d | | d | | |	 | | | d | | d | | d |
 | f ƒ qÊ Wn  d  S(   Nt   wsB   %4d%4d%4d %10.6f %10.6f %4d%4d%4d %10.6f %10.6f %4d%4d%4d %10.3f 
i    i   i   (   R   t   openR   R3   R   R   RO   R4   t   phasest   xrangeR@   t   write(   R   RX   t   filet   ict   it   iot   fcdt   fcpt   fdt   fpt   fodt   stt   j(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   print_all_reflections_in_file™   s    8/N(
   t   __name__t
   __module__R   R   R   RT   RU   RV   RY   Rj   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyR      s   	L			c         C   s   t  |  ƒ j ƒ  } | j ƒ  } | j ƒ  } | j ƒ  } | } x< t d ƒ D]. } | | | t j | | | d ƒ 7} qI W| S(   Ni   g      @(   R	   t   fetcht
   array_of_at
   array_of_bt   cR]   t   matht   exp(   t   absent_atom_typet   ssR?   t   a_wkt   b_wkt   c_wkt	   result_wkRa   (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   form_factor·   s    ,c         C   sé   |  j  ƒ  s t ‚ |  j ƒ  s% t ‚ t j |  j ƒ  ƒ } t j |  t j	 | j
 ƒ  ƒ j | j ƒ  ƒ ƒ } | j | ƒ } t j | ƒ j ƒ  | j ƒ  j ƒ  } t j |  j ƒ  ƒ j ƒ  | j ƒ  j ƒ  } | | k sÛ t ‚ | | } | S(   N(   t
   is_0_basedR   t	   is_paddedR   t   real_to_complex_3dt   focusR   t   copyR   t   gridt   m_realt	   set_focusR   t   forwardR   t   colt   productR!   t   volume(   t   mask_mapR   t   nxyzt   fft_managert   padded_dataRS   t   scalet   sc(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyRD   Ä   s    	%+
c         C   s›   |  j  ƒ  j ƒ  } | | } |  j ƒ  | } |  j ƒ  j ƒ  } t | ƒ j ƒ  } | j | ƒ }	 |	 t j | d | ƒ }
 t	 j
 d |  d | |
 ƒ } | S(   Ng      @R0   R4   (   R+   t   order_zR4   t	   d_star_sqR	   Rm   t   at_d_star_sqR   Rr   R   RJ   (   t   ft   n_water_atoms_absentt   bf_atoms_absentRs   t   nsymt   n_lost_wR4   t   d_star_sq_dataR?   t   fft   factort   f_by_m(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   f_ordered_solventÒ   s    
c         C   sJ  |  j  ƒ  j ƒ  } d t j |  j ƒ  j ƒ  ƒ } | | }	 | | }
 | | } t j |  j ƒ  ƒ } t j d | | d t j	 d ƒ } |  j
 ƒ  j ƒ  } t | | ƒ s± t ‚ t | ƒ j ƒ  } | j | ƒ } | t j | d | ƒ } d | | |	 |
 | d | | | | } |  j d | ƒ } |  j d | ƒ } | | f S(   Ng      ð?g      Ð¿i   i   g      @R4   (   R+   RŒ   R   t   pow2t
   d_spacingsR4   RO   Rr   Rq   t   piR�   R   R   R	   Rm   RŽ   RJ   (   t   f_distt   n_atoms_includedt   n_nonwater_atoms_absentR�   R‘   t   final_errorRs   R’   Rt   t   n_partt   n_lost_pR“   t   f_dist_datat   a_dR”   R?   R•   R–   t   b_dt   alphat   beta(    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt
   alpha_betaà   s     


&.(   t
   __future__R    Rq   t   cctbx.array_familyR   t   cctbx.eltbxR   t   cctbxR   R   t   libtbx.test_utilsR   R   t   scitbxR   R   t   cctbx.eltbx.xray_scatteringR	   t   boost.pythont   boostt   pythont
   import_extt   extR
   R   t   objectR   Ry   RD   R˜   R§   (    (    (    sP   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/max_lik/max_like_non_uniform.pyt   <module>   s*   

 			